Interpretive Summary: The question of how the bacterium called Mycobacterium avium subspecies paratuberculosis (MAP) can cause Johne’s disease remains largely unanswered. One major reason for this knowledge gap is that the organism is difficult to work with. In this paper we attempt to bring some clarity to the question of how MAP causes disease. We know for certain that MAP needs iron to grow inside the animal, so we looked at how it responds when iron is limiting, which is the condition inside the host animal. By examining the all genes that the bacterium expresses while iron is limiting, we discovered a surprising result. The MAP strains that preferentially infect sheep cannot store iron! This was not the case for cattle strains. This is important because we now have some clues about the genes that enable iron storage. Furthermore, we might have a clue as to why sheep strains grow so poorly compared to cattle strains. This paper is of primary interest to scientists who will build on this information to prevent infection and subsequent disease.

Technical Abstract:
Background: Two genotypically and microbiologically distinct strains of Mycobacterium avium subsp. paratuberculosis (MAP) exist – the type I and type II strains that primarily infect sheep and cattle, respectively. Concentration of iron in the cultivation medium has been suggested as one contributing factor for the observed microbiologic differences. We recently demonstrated that type I strains have defective iron storage systems, leading us to propose that these strains might experience iron toxicity when excess iron is provided in the medium. To test this hypothesis, we carried out transcriptional and proteomic profiling of these MAP strains under iron-replete or –deplete conditions.
RESULTS: We first complemented M.smegmatis'ideR with IdeR of type II MAP or that derived from type I MAP and compared their transcription profiles using M. smegmatis mc2155 microarrays. In the presence of iron, type I IdeR repressed expression of bfrA and MAP2073c, a ferritin domain containing protein suggesting that transcriptional control of iron storage may be defective in type I strain. We next performed transcriptional and proteomic profiling of the two strain types of MAP under iron-deplete and –replete conditions. Under iron-replete conditions, type II strain upregulated iron storage (BfrA), virulence associated (Esx-5 and antigen85 complex), and ribosomal proteins. In striking contrast, type I strain downregulated these proteins under iron-replete conditions. iTRAQ (isobaric tag for relative and absolute quantitation) based protein quantitation resulted in the identification of four unannotated proteins. Two of these were upregulated by a type II MAP strain in response to iron supplementation. The iron-sparing response to iron limitation was unique to the type II strain as evidenced by repression of non-essential iron utilization enzymes (aconitase and succinate dehydrogenase) and upregulation of proteins of essential function (iron transport, [Fe-S] cluster biogenesis and cell division).
CONCLUSIONS: Taken together, our study revealed that type II and type I strains of MAP utilize divergent metabolic pathways to accommodate in vitro iron stress. The knowledge of the metabolic pathways these divergent responses play a role in are important to 1) advance our ability to culture the two different strains of MAP efficiently, 2) aid in diagnosis and control of Johne’s disease, and 3) advance our understanding of MAP virulence.